view README @ 10:d247213cebfc draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"

Galaxy wrappers for the Mothur metagenomics tools (http://www.mothur.org/wiki/Main_Page)

The Mothur Tool Suite repository:
	- Provides Mothur wrappers for the Mothur tools
	- Downloads and builds Mothur and all its dependencies on the Linux or Mac operating system

Installing Tools via the API:
This is a rather large tool suite, if you are having problems installing via the toolshed, try using the API instead
    - Install ephemeris: pip install ephemeris -U
    - Use ephemeris to install tools: shed_install -a <your admin API key> -t tools.yaml
    - (You can find a tools.yaml you can use in this repo as well)

Installing reference data from silva and greengenes:
    - There is a Galaxy datamanager for available for Mothur

 RDP reference file (modified for mothur):
  http://www.mothur.org/wiki/RDP_reference_files
   - 16S rRNA reference (RDP): A collection of 9,662 bacterial and 384 archaeal 16S rRNA gene sequences with an improved taxonomy compared to version 6.
     http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip
   - 16S rRNA reference (PDS): The RDP reference with three sequences reversed and 119 mitochondrial 16S rRNA gene sequences added as members of the Rickettsiales
     http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip
   - 28S rRNA reference (RDP): A collection of 8506 reference 28S rRNA gene sequences from the Fungi that were curated by the Kuske lab
     http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip
 Silva reference:
  http://www.mothur.org/wiki/Silva_reference_files
  - Bacterial references (14,956 sequences)
    http://www.mothur.org/w/images/9/98/Silva.bacteria.zip
  - Archaeal references (2,297 sequences)
    http://www.mothur.org/w/images/3/3c/Silva.archaea.zip
  - Eukaryotic references (1,238 sequences)
    http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip
  - Silva-based alignment of template file for chimera.slayer (5,181 sequences)
    http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
 Alignment database rRNA gene sequences:
  http://www.mothur.org/wiki/Alignment_database
  - greengenes reference alignment
    http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip
  - SILVA (Silva reference)
    http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
 Secondary structure mapping files:
  http://www.mothur.org/wiki/Secondary_structure_map
    http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip
    http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip
 Lane masks:
  http://www.mothur.org/wiki/Lane_mask
  greengenes-compatible mask:
     - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database
       http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter
     - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database
       http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter
     - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper
       http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter
  SILVA-compatible mask:
     - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper
       http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter
 Lookup Files for sff flow analysis using shhh.flows:
  http://www.mothur.org/wiki/Alignment_database